YuLab-SMU/biomedical-knowledge-mining-book YuLab-SMU/biomedical-knowledge-mining-book

  • Stars
    star
    69
  • Rank 452,630 (Top 9 %)
  • Language
    TeX
  • Created almost 6 years ago
  • Updated over 1 year ago
Twitter logo Share LinkedIn logo Share Facebook logo Share
YuLab-SMU/biomedical-knowledge-mining-book
github

YuLab-SMU

Reviews

There are no reviews yet. Be the first to send feedback to the community and the maintainers!

Repository Details

๐Ÿ“š Biomedical knowledge mining using GOSemSim and clusterProfiler

More Repositories

1

clusterProfiler

๐Ÿ“Š A universal enrichment tool for interpreting omics data
R
1,004
star
2

ggtree

๐ŸŽ„Visualization and annotation of phylogenetic trees
R
834
star
3

enrichplot

Visualization of Functional Enrichment Result
R
226
star
4

ChIPseeker

๐ŸŽฏ ChIP peak Annotation, Comparison and Visualization
R
220
star
5

ggmsa

๐Ÿšฅ Visualizing publication-quality multiple sequence alignment using ggplot2
R
200
star
6

MicrobiotaProcess

๐Ÿฆ  A comprehensive R package for deep mining microbiome
R
178
star
7

ggbreak

๐Ÿ’” An implementation of scale functions for setting axis breaks of a 'gg' plot.
R
127
star
8

DOSE

๐Ÿ˜ท Disease Ontology Semantic and Enrichment analysis
R
114
star
9

treedata-book

๐Ÿ“š a complete reference book for treeio, tidytree and ggtree packages
TeX
100
star
10

aplot

Decorate a plot with associated information
R
97
star
11

treeio

๐ŸŒฑ Base Classes and Functions for Phylogenetic Tree Input and Output
R
94
star
12

ggtreeExtra

๐Ÿ‹ Add Geom Layers On Circular Or Other Layout Tree Of โ€œggtreeโ€
R
86
star
13

scatterpie

๐ŸŽจ scatter pie plot
R
60
star
14

createKEGGdb

Create KEGG.db Package
R
58
star
15

GOSemSim

โ›ณ GO-terms Semantic Similarity Measures
R
58
star
16

plotbb

๐Ÿ–Œ๏ธ Grammar of Graphics for base plot
R
52
star
17

tidytree

๐ŸšฟA Tidy Tool for Phylogenetic Tree Data Manipulation
R
51
star
18

fanyi

Translate Words or Sentences via Online Translators
R
44
star
19

ggsc

๐Ÿง  Visualizing Single Cell and Spatial Transcriptomics
R
40
star
20

ReactomePA

Reactome Pathway Analysis
R
37
star
21

MicrobiomeProfiler

๐Ÿฆ  A shiny package for microbiome functional enrichment analysis
R
36
star
22

ProjectYulab

โญ๏ธ Small coding tasks that enable you to participate in our development
33
star
23

yulab.utils

Miscellaneous functions commonly used by 'YuLab-SMU'.
R
30
star
24

treedataverse

Meta package for processing and visualizing tree with data
R
27
star
25

plotting-tree-with-data-using-ggtreeExtra

TeX
24
star
26

tigeR

๐Ÿฏ tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package
R
24
star
27

GeoTcgaData

Processed rna-seq data, copy number variation data, and methylation data on GEO and TCGA
R
22
star
28

seqcombo

Visualization tool for genetic reassortment
R
21
star
29

nCov2019

๐Ÿฆ  Exploring COVID-19 data
R
19
star
30

ggfun

useful functions for ggplot
R
18
star
31

wget

download files in R using wget -c
R
17
star
32

survival-guide

YuLab็š„็”Ÿๅญ˜็ง˜็ฌˆ
16
star
33

clusterProfiler.dplyr

dplyr verbs for clusterProfiler outputs
R
13
star
34

TDbook

A Companion Package for the Book "Data Integration, Manipulation and Visualization of Phylogenetic Trees"
R
13
star
35

tidydr

R
13
star
36

MMINP

Microbe-Metabolite INteractions-based metabolic profiles Predictor
R
13
star
37

clusterProfiler-book

a complete reference book for clusterProfiler and its sub-packages
TeX
13
star
38

ggtreeDendro

Drawing 'dendrogram' using 'ggtree'
R
12
star
39

yulab-smu.github.io

๐Ÿ  Homepage for YuLab-SMU
HTML
12
star
40

meshes

๐Ÿฉบ MeSH Enrichment and Semantic analyses
R
11
star
41

clusterProfiler_protocol

omics data analysis using clusterProfiler ;)
R
10
star
42

MicrobiotaProcessWorkshop

The workshop of microbiome datasets analysis using MicrobiotaProcess
Makefile
9
star
43

shinyTempSignal

Explore Temporal and Other Phylogenetic Signals
R
9
star
44

ggflow

Draw flow chart based on ggtree
R
8
star
45

mirrorselect

To help select CRAN and Bioconductor mirrors.
R
8
star
46

aplotExtra

Creating composite plot using 'aplot'
R
8
star
47

rdpvis

Visualizing sequence break point
R
7
star
48

sc2p

single cell to pathway
R
6
star
49

iggtree

interactive tree viewer using ggtree + shiny
R
6
star
50

learnggtree

Tutorial for Learning 'ggtree'
Makefile
6
star
51

seqmagick

sequence manipulation
R
6
star
52

supplemental-clusterProfiler-v4

TeX
5
star
53

ggtreeSpace

๐Ÿ•ธ๏ธExploring phylomorphospace using 'ggtree'
R
5
star
54

wikiprofiler

R
5
star
55

supplemental-ggbreak

TeX
5
star
56

SVP

R
5
star
57

msacolor

R
4
star
58

HDO.db

A new version of DO.db
R
4
star
59

simpleGO

Simple GO Enrichment Analysis
R
4
star
60

BMplot

Base Modification Visualization
R
4
star
61

MP_supplementary_file

R
4
star
62

ggcircos

R
4
star
63

misc

3
star
64

ggmsaBioWorkshop2021

Dockerfile
3
star
65

multiEnrichment

multi-omic enrichment analysis
R
3
star
66

ggtangle

Draw Network with Data
R
3
star
67

gson

R
2
star
68

lab_dot_files

Vim Script
2
star
69

sclet

R
1
star
70

MPO.db

R
1
star
71

mh_analysis

R
1
star
72

ChIPseeker_current_protocols

1
star
73

gson-files

HTML
1
star
74

ggacmap

plotting acmap using ggplot2
R
1
star
75

HPO.db

R
1
star
76

COSemSim

An R package measures semantic similarity value for cell types, genes and proteins
R
1
star
77

supplemental-ggmsa

R
1
star